What happens beneath our cities before wastewater even reaches the treatment plant? This study uncovers how microbes thriving inside sewer networks play a decisive role in shaping the microbial communities that drive wastewater treatment and resource recovery. Wastewater treatment plants (WWTPs) and sewer systems are tightly connected but the microbial link between them is largely unexplored. This study presents the first comprehensive, species-level study of the sewer microbiome, spanning biofilms, sediments, and wastewater from domestic gravity and pressure sewers in Aalborg, Denmark. By comparing these communities with samples from influent wastewater and activated sludge from downstream WWTPs, the origins of most process-critical bacterial species were found. Activated sludge is the cornerstone of pollutant removal and resource recovery in WWTPs worldwide, so understanding the key factors controlling community assembly is vital for improving plant stability and performance.
The results reveal that many process-critical bacteria essential for WWTP performance are not born in the activated sludge tanks themselves: They originate from sewers. This finding builds on the growing recognition that microbial immigration from incoming wastewater is a key driver of community assembly in activated sludge systems. These sewer communities include species linked to critical processes such as nitrogen and phosphorus removal. Within the sewer network, a clear gradient was observed: gut-associated bacteria dominate the upstream wastewater, while biofilm and sediment-associated bacteria prevail closer to the WWTP inlets. Rain events further shape this balance by washing biofilm-associated bacteria toward the treatment plant, dynamically altering the microbial mix that seeds the treatment plant. In the activated sludge tanks, gut bacteria die off, while taxa from the sewer microbiome thrive as part of the process-critical community.
The study provides a holistic view of the urban wastewater systems and redefines how we view the urban water microbiome. Sewers are not just pipelines; they are dynamic microbial habitats that everyday produce and convey biomass corresponding to 5-10% of the biomass in the downstream activated sludge tanks. They also act as a strong environmental species-filtration step before wastewater reaches treatment facilities. Recognizing the sewer microbiome as a key source community helps explaining why activated sludge communities differ across regions and countries and underscores the importance of understanding sewer networks and the diversity of these as part of the broader wastewater treatment ecosystem.
Read the full journal article titled Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants in The ISME Journal. This article has been selected as Editor’s Choice for the month of September 2025.
Authors
- Marie Riisgaard-Jensen, Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Rodrigo Maia Valença, Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Miriam Peces, Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Per Halkjær Nielsen, Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark